It's nice to have allies in her family (I wish I had that!), but try to make sure that your MIL isn't pressuring your wife to give up her affair and work on your marriage. It's just going to make her feel judged, and could cause her to further isolate herself from you and and her parent(s). You want as many roads back open as possible, and her family is one of those roads.
Her mother/parents can choose not to support her affair, or any relationship she may have with a woman, but it's important that that not also come with a side serving of not supporting her. She will need support at some point in time, and she won't feel like she can turn to your or your MIL if she's felt pressure from you guys (even pressure by proxy) while going through this.
"I love you, and I'm here for you no matter what" is the implicit parent-child contract. It's not "I'm here for your relationship I disapprove of". Likewise, "I disapprove of your relationship" isn't "I disapprove of you", but sometimes it really feels like it. Your MIL may need to express that to your wife explicitly at some point in order to keep that road home open.
Me: 31 W: 31 T: 10 years CL: 7 years IDLY: 01/13 Sep: 07/13 I Moved out: 10/13 W Currently seeing OM Pets, but No Children